Background Deafferentation pain is a kind of chronic pain syndrome and hard to manipulate. To evaluate the effectiveness and safety of junctional dorsal root entry zone (DREZ) coagulation, 23 consecutive patients with intractable deafferentation pain syndrome were studied. Methods Twenty-three patients underwent junctional DREZ coagulation (C5-T1 for upper extremities and L2-S1 for lower extremities) under general anesthesia. The pain severity was evaluated by the short McGill pain questionnaire (MPQ) and the visual analog scale (VAS), and the depression and anxiety of patients were assessed by Hamilton rating scale for depression (HRSD), Hamilton anxiety scale (HAMA), self-rating anxiety scale (SAS) and self-rating depression scale (SDS). Results All the patients experienced significant pain reduction immediately after surgery. The scales of short MPQ and VAS at pre-operation, 6-month and 12-month follow-up were 31.5 +/- 3.4 and 8.8 +/- 1.5, 6.5 +/- 1.9 and 2.5 +/- 2.2, 7.1 +/- 2.1 and 2.9 +/- 1.9, respectively. The postoperative scores comparing to pre-operative scores showed a statistically significant difference (P<0.01). The depression and anxiety state was also significantly relieved. At 12-month follow-up 6 patients had complete pain relief, 11 had excellent results with more than 75% pain relief, 17 had good results with more than 50% pain relief (73.9%). The main postoperative complications were transient slight hemiplegia (8), hypesthesia and paresthesia (15), a bearing down feeling of affected extremity (6), and deep sensory disability in the lower limbs (4) on the operated side. Because of the long time and prone position of the operation, 13 cases had a transient hyperalgesia in the upper chest. Conclusion DREZ coagulation is a safe and effective procedure in the treatment of deafferentation pain syndromes.